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- PDB-4k1w: Crystal structure of the A314P mutant of mannonate dehydratase fr... -

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Basic information

Entry
Database: PDB / ID: 4k1w
TitleCrystal structure of the A314P mutant of mannonate dehydratase from novosphingobium aromaticivorans complexed with mg and d-mannonate
ComponentsMandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
KeywordsISOMERASE / Enolase fold / MANNONATE DEHYDRATASE / D-MANNONATE
Function / homology
Function and homology information


mannonate dehydratase / mannonate dehydratase activity / amino acid catabolic process / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
D-mannonate dehydratase / : / D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain ...D-mannonate dehydratase / : / D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBON DIOXIDE / CARBONATE ION / D-MANNONIC ACID / 1,3-PROPANDIOL / TRIETHYLENE GLYCOL / D-mannonate dehydratase
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.646 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of the A314P mutant of mannonate dehydratase from novosphingobium aromaticivorans complexed with mg and d-mannonate
Authors: Fedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
History
DepositionApr 6, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionApr 9, 2014ID: 3R4E
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
C: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
D: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,62127
Polymers188,5304
Non-polymers2,09123
Water18,0691003
1
A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,27113
Polymers94,2652
Non-polymers1,00611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-33 kcal/mol
Surface area26770 Å2
MethodPISA
2
C: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
D: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,35014
Polymers94,2652
Non-polymers1,08512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-32 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.223, 165.363, 167.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-651-

HOH

21B-860-

HOH

31C-659-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein


Mass: 47132.395 Da / Num. of mol.: 4 / Mutation: A314P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: Saro_3675 / Production host: Escherichia coli (E. coli) / References: UniProt: A4XF23

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Non-polymers , 7 types, 1026 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CS2 / D-MANNONIC ACID / D-MANNONATE


Mass: 196.155 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O7
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CO2
#6: Chemical
ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#7: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1003 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG400, 0.1M HEPES, 0.2M SODIUM CHLORIDE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.646→46.214 Å / Num. all: 191348 / Num. obs: 191348 / % possible obs: 98.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
BALBESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QJJ

2qjj


Resolution: 1.646→46.214 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 18.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1836 9615 5.02 %RANDOM
Rwork0.1569 ---
all0.1582 191348 --
obs0.1582 191348 98.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.646→46.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12325 0 136 1003 13464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612905
X-RAY DIFFRACTIONf_angle_d1.0717555
X-RAY DIFFRACTIONf_dihedral_angle_d12.934750
X-RAY DIFFRACTIONf_chiral_restr0.0741885
X-RAY DIFFRACTIONf_plane_restr0.0062264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6457-1.66440.28212620.26665279X-RAY DIFFRACTION87
1.6644-1.6840.30723270.26155980X-RAY DIFFRACTION98
1.684-1.70450.29292900.25235962X-RAY DIFFRACTION98
1.7045-1.72610.26673000.23426003X-RAY DIFFRACTION99
1.7261-1.74880.25063730.2245952X-RAY DIFFRACTION99
1.7488-1.77280.25663120.2186026X-RAY DIFFRACTION99
1.7728-1.79810.23353210.20615985X-RAY DIFFRACTION99
1.7981-1.8250.22063210.1975997X-RAY DIFFRACTION99
1.825-1.85350.23282830.17876053X-RAY DIFFRACTION99
1.8535-1.88390.18612970.17026061X-RAY DIFFRACTION99
1.8839-1.91640.22643200.1756033X-RAY DIFFRACTION99
1.9164-1.95120.21643070.17276048X-RAY DIFFRACTION99
1.9512-1.98870.22883480.17246033X-RAY DIFFRACTION99
1.9887-2.02930.19833420.16466020X-RAY DIFFRACTION99
2.0293-2.07340.20913000.1586096X-RAY DIFFRACTION99
2.0734-2.12170.19293200.15996073X-RAY DIFFRACTION99
2.1217-2.17470.19243230.15276029X-RAY DIFFRACTION99
2.1747-2.23350.18423260.14746097X-RAY DIFFRACTION100
2.2335-2.29930.18323090.1536141X-RAY DIFFRACTION100
2.2993-2.37350.19183250.15316053X-RAY DIFFRACTION100
2.3735-2.45830.17683380.156122X-RAY DIFFRACTION100
2.4583-2.55670.18143400.14676084X-RAY DIFFRACTION100
2.5567-2.67310.18683360.15136125X-RAY DIFFRACTION100
2.6731-2.8140.183320.15026126X-RAY DIFFRACTION100
2.814-2.99020.18923250.16176142X-RAY DIFFRACTION100
2.9902-3.22110.18493140.15976179X-RAY DIFFRACTION100
3.2211-3.54510.16573220.14796181X-RAY DIFFRACTION100
3.5451-4.05780.14233350.13416201X-RAY DIFFRACTION100
4.0578-5.11140.1483230.1286245X-RAY DIFFRACTION100
5.1114-46.2320.17423440.16026407X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9931-0.00350.26080.6273-0.15560.5672-0.003-0.2746-0.07930.2119-0.02910.01950.0597-0.05340.03340.2261-0.01170.03140.246-0.01440.1037-8.960430.8785-11.7862
20.67580.0803-0.03910.9254-0.08080.39940.0064-0.1263-0.1260.1349-0.0524-0.14910.05260.05740.0420.14530.0228-0.01820.15220.04670.149315.021316.448-29.6524
30.90230.03740.01920.8307-0.02420.5286-0.0895-0.2290.44640.18590.00620.0235-0.1478-0.06460.05940.22890.0504-0.08980.1672-0.12950.3851-11.321772.8226-26.265
40.7070.0607-0.02220.6397-0.05430.8311-0.0368-0.22280.29440.1794-0.0822-0.1381-0.1820.08460.07340.2335-0.0263-0.12720.2564-0.06120.264216.81358.5405-15.5994
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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